Merge branch 'main' into main

Author: grst

.pre-commit-config.yaml

@@ -23,13 +23,13 @@ repos:
       - id: prettier
   # package metadata
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.36.1
+    rev: 0.37.0
     hooks:
       - id: check-jsonschema
         files: "scripts/src/ecosystem_scripts/schema.json"
         args: ["--check-metaschema"]
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.36.1
+    rev: 0.37.0
     hooks:
       - id: check-jsonschema
         files: "packages/.*/meta.yaml"
@@ -45,15 +45,15 @@ repos:
         exclude: "^packages/.*/(meta.yaml|logo\\..*)$"
   # scripts
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.14
+    rev: v0.15.5
     hooks:
       - id: ruff-check
         args: [--fix, --exit-non-zero-on-fix]
         files: ^scripts/.*$
       - id: ruff-format
         files: ^scripts/.*$
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.12.1
+    rev: v2.16.2
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/camptocamp/jsonschema-gentypes

packages/anndataR/meta.yaml

@@ -4,7 +4,7 @@ description: |
   of H5AD files and conversion to common R data structures.
 project_home: https://github.com/scverse/anndataR
 documentation_home: https://bioconductor.org/packages/anndataR/
-tutorials_home: https://anndatar.data-intuitive.com/
+tutorials_home: https://scverse.org/anndataR/
 install:
   bioconductor: anndataR
 license: MIT

packages/nichepca/meta.yaml

@@ -0,0 +1,20 @@
+name: nichepca
+description: |
+  A Python package for PCA-based spatial domain identification in single-cell spatial transcriptomics data.
+project_home: https://github.com/imsb-uke/nichepca
+documentation_home: https://nichepca.readthedocs.io/
+tutorials_home: https://nichepca.readthedocs.io/page/notebooks/example.html
+install:
+  pypi: nichepca
+tags:
+  - spatial-omics
+  - spatial domain identification
+  - spatial clustering
+license: MIT
+version: v0.0.3
+contact:
+  - dschaub95
+test_command: |
+  uv sync --all-extras && \
+  uv run pytest .
+category: ecosystem

scripts/pyproject.toml

@@ -1,6 +1,5 @@
 [build-system]
 build-backend = "hatchling.build"
-
 requires = [ "hatch-vcs", "hatchling" ]
 
 [project]
@@ -29,19 +28,16 @@ dependencies = [
   "pyyaml",
   "rich",
 ]
-
 urls.Documentation = "https://github.com/scverse/ecosystem-packages#readme"
 urls.Issues = "https://github.com/scverse/ecosystem-packages/issues"
 urls.Source = "https://github.com/scverse/ecosystem-packages"
 scripts.register-template-repos = "ecosystem_scripts.template_repo_registry:main"
 scripts.validate-registry = "ecosystem_scripts.validate_registry:main"
 
-[tool.hatch.envs.default]
-python = "3.13"
-
-[tool.hatch.version]
-source = "vcs"
-fallback-version = "0.0"
+[tool.hatch]
+envs.default.python = "3.13"
+version.source = "vcs"
+version.fallback-version = "0.0"
 
 [tool.ruff]
 line-length = 120
@@ -72,7 +68,7 @@ lint.select = [
   "W",
   "YTT",
 ]
-lint.ignore = [  ]
+lint.ignore = []
 
 [tool.mypy]
 strict = true

scripts/src/ecosystem_scripts/validate_registry.py

@@ -6,6 +6,7 @@
 import argparse
 import json
 import os
+import re
 import shutil
 import sys
 from collections import defaultdict
@@ -48,6 +49,11 @@ def append(self, obj: Exception | None) -> None:
         return super().append(obj)
 
 
+RE_RTD = re.compile(
+    r"https?://(?P<domain>.*\.(?:readthedocs\.io|rtfd\.io|readthedocs-hosted\.com))/(?P<version>en/[^/]+)(?P<path>.*)"
+)
+
+
 class LinkChecker:
     """Track known links and validate URLs."""
 
@@ -65,6 +71,12 @@ def check_and_register(self, url: str, context: str) -> None | ValidationError:
         context
             Context information for error messages (e.g., file being validated)
         """
+        if m := re.fullmatch(RE_RTD, url):
+            new_url = f"https://{m['domain']}/" + (f"page{m['path']}" if m["path"].strip("/") else "")
+            msg = (
+                f"Please use the default version in ReadTheDocs URLs instead of {m['version']!r}:\n{url}\n->\n{new_url}"
+            )
+            return ValidationError(msg)
         if url in self.known_links:
             msg = f"{context}: Duplicate link: {url}"
             return ValidationError(msg)

template-repos.yml

@@ -46,6 +46,7 @@
 - url: https://github.com/bunina-lab/scDoRI_tools
 - url: https://github.com/cameronraysmith/perturbvelo
 - url: https://github.com/carmonalab/pyucell
+- url: https://github.com/cellannotation/pairOT
 - url: https://github.com/clinicalomx/napari-prism
 - url: https://github.com/cobioda/scispy
 - url: https://github.com/const-ae/pyLemur
@@ -115,6 +116,7 @@
 - url: https://github.com/scverse/pytometry
 - url: https://github.com/scverse/scanpy
 - url: https://github.com/scverse/scirpy
+- url: https://github.com/scverse/scverse-misc
 - url: https://github.com/scverse/scverse-tutorials
 - url: https://github.com/scverse/simple-scvi
 - url: https://github.com/scverse/spatial-sample-aggregation
@@ -142,6 +144,7 @@
 - url: https://github.com/theislab/troutpy
 - url: https://github.com/timtreis/gefslim
 - url: https://github.com/vitkl/cell2module
+- url: https://github.com/vitkl/regularizedvi
 - url: https://github.com/wangd12rpi/hescape_changed
 - url: https://github.com/yizhak-lab-ccg/scXpand
 - url: https://github.com/zunderlab/eschr